G'day Cookie, I'll have a go at this question...
There is a clear, and in some cases, marked difference when you taste the same batch of beer out of a bottle compared to the kegged quantity. It's partially about carbonation - I'll assume that you don't have a system that is able to carbonate the kegged beer at exactly the same pressure as what's in your bottles, or vice versa - but I believe it's more about the flavour properties of beer in larger (kegged) versus smaller (bottled) volumes and the conditioning that occurs in the larger vessel. Now, I know you're already thinking that this assertion is irrelevant in relation to commercial beers that have been pasteurised and filtered etc before packaging.
My thoughts are, at this stage anyway, limited to what we experience when we drink beer out of a keg that has yeast in it, and compare that flavour profile to the same batch of beer that's been bottle conditioned, presumably with the same yeast as what's in the keg. A well known advantage of kegged beer is the potential benefit you have in relation to bulk conditioning. Then again, I've had beers dramatically lower in quality in a keg and when I've had a bottle of the same batch, the beer's nice and clean. My palate detects a noticeable decrease in hop bitterness and flavour in a keg compared to the exact same batch in bottles, over time.
CO2 is well known for increasing the relative bitterness / sharpness in a beer. You may have perceived a difference if the keg was less carbonated compared to what you drank out of the bottle - I doubt that the CO2 would have tasted different in each case, due to the CO2 itself. Often, it's simply the case that the brewer used a short chain sugar (eg, Dextrose) which tends to add a slightly dryer / sharper flavour profile to stubbies of beer compared to a keg of the same batch.
Cheers,
TL